Table II. Estimation of nonenzymatic deamidated peptides and N-glycopeptides in five groups of proteomic data.
| ERLIC1-RPc | ERLIC2-RPc | ERLIC3-RPd | ERLIC4-RPd | In-Gel-RP | |
|---|---|---|---|---|---|
| Unique peptides | 17003 | 16518 | 10396 | 11939 | 5267 |
| Unique glycopeptidesa | 96 | 108 | 107 | 781 | 35 |
| Unique Asn-deamidated peptides | 815 | 845 | 821 | 1020 | 288 |
| Ratio of Asn-deamidationb | 4.79% | 5.12% | 7.90% | 8.54% | 5.45% |
| Unique Gln-deamidated peptides | 320 | 366 | 307 | 418 | 89 |
| Ratio of Gln-deamidationb | 1.88% | 2.22% | 2.95% | 3.50% | 1.69% |
a It should be noted that all N-glycopeptides identified in ERLIC1-RP, ERLIC2-RP, ERLIC3-RP, and In-Gel-RP are false positive ones because these samples were not treated with PNGase F to remove N-glycans.
b Ratio of deamidation is calculated as the number of unique deamidated peptides divided by that of all identified unique peptides in the run.
c ERLIC1-RP and ERLIC2-RP were two replicates for whole proteome analysis.
d ERLIC3-RP and ERLIC4-RP were used for the concurrent analysis of proteome, phosphoproteome and glycoproteome. The only difference between them was that ERLIC4-RP was deglycosylated with PNGase F, but ERLIC3-RP was not.